I used to think that incest was only in hentai/eroge, but gradually, I have run into more mainstream content which seems to hint at brother-sister, mother-son relationships, or the tension of such attraction.
What is the origin of this theme?
Why is it so prevalent in Japanese manga and anime compared to Western comics?
It seems strange for a taboo to be popping up everywhere, so I am curious as to the origin.
First, it needs to be said that incest in popular culture is prevalent in many other culture. It isn't unique to anime or manga works. Although it is true that compared to Western comics it is less prevalent, incest do exist in Western pop-culture songs, movies, literature, etc.
With that, we should focus on what it is in Japanese culture that makes incest a seemingly prevalent trope in anime and manga. There's also different types of incest relationships.
Incest is a taboo in Japan. What is incest to them, however, may be a little bit different than ours. Incest marriages between cousins are occasional as they are not considered incestuous until recently. This may explain why incest relationships like in Elfen Lied is a recurring trope.
Another thing is that historically, marriages between nephews and nieces have been approved. Even now in some rural areas, fathers marry their daughters when the mother dies. They are forced to do this as they follow old feudal laws. Sometimes when both parents died, the brother ends up having sex with the sister in order to end confusion.
There's also the common trope of brothers and sisters sleeping or bathing together in anime and manga. This is easily explained as such things are still prevalent in Japanese society. This doesn't necessarily lead to incest, however, but there are certainly hints towards it.
The first manga that involves incest is Cream Lemon, released in the 1980s. So this isn't something new. It is also noted that incest is in mangas for the Shoujo demographics, which is mainly for females. In other words, people might like incestuous anime and manga for the emotional relationship and not the physical relationships.
The combination of Japanese history and the demographic's tastes may help explain why incest is a popular trope in anime and manga. I could go on and on, but it may take too long to explain, so if anyone would like to read more, I have provided sources for others.
Sources:
http://en.wikipedia.org/wiki/Incest_in_popular_culture
http://www.mangatherapy.com/post/1467868478/incest-in-anime-manga
http://psychohistory.com/articles/the-universality-of-incest/
Can you name some titles that features "true" incest between biological siblings? Incest is definitely a taboo at least in modern Japan. There are only a few love stories about incest between biological siblings, and most Japanese otaku do not like them.
However, a sibling-in-law is a notable exception. The Japanese law allows the marriage of two siblings-in-law as long as they are not related by blood. For example, at least legally speaking, a biological son of A and B can marry an adopted daughter of A and B. This is prohibited in many other parts of the world, and it is strongly frowned upon in reality also in Japan. But in fiction, this works as an ideal setting for a Japanese-style romantic comedy, where the author has to depict an almost never-ending unanswered/secret love and provide many "service cuts".
One of the early works that successfully took advantage of this fact is Marmalade Boy, where an adolescent girl is suddenly forced to live with a new handsome brother(-in-law), who she eventually falls in love with. People enjoyed this legally-valid-but-ethically-forbidden love. It has become a popular story trope, and many works including Da Capo, Sister Princess, Kissxsis, ImoCho and Eromanga Sensei use similar settings.
EDIT: Perhaps it's worth taking a look at the Amazon reviews of the last volume of OreImo, which is undoubtedly one of the most famous light novels in the "little sister" genre. You can see many readers were disappointed and turned off when the relationship between the protagonist and his (biological) little sister turned out to be "(romantic) love" at this point. It shows true unambiguous incest is unacceptable even to many fans of this genre.
Reference:
Despite the name, Little Sister Heroine attempts to mitigate the obvious incestuous fallout; they're usually either a step sister, adopted or, more rarely, technically a cousin or distant relation.
